This is my going through your notes and commenting on things I felt the need to comment on. It will be very long, and I'm sure there will be more in the future, but for now:

CROP FRAME WHEREVER POSSIBLE TO REMOVE ANAKIN’S PONYTAIL
A noble idea, but futile when it comes down to it. It's impossible to remove in every shot, and Obi-Wan's will br prominent in Episode I as well. So I would say don't concern yourself too much with this.

CUT ALL UTTERANCES OF “MOM” and “DAD”, and “BOYFRIEND/GIRLFRIEND”

I agree, these casual references to people just don't seem right for these characters in these circumstances.

REMOVE “ANNIE” EXCEPT FOR SHMI

I think I suggested this, but maybe we both thought of it independently. Anyway, this is a MUST for the entire PT.

Conference Room Scene Suggestion:
(This is a bit different from yours. Notice Padme does not ask "Do you have any idea who's behind this attack," because Mace's answer would be total BS. Don't ask, don't tell.)
EXT. Chancellor's office - Day
INT. Chancellor's office - Continuous
Ki-Adi-Mundi: He is a political idealist, not a murderer.
Mace: You know Dooku was once a jedi. He couldn't assassinate anyone.
Palpatine: But more and more star systems are joining the seperatists. I don't know how much longer I can hold off...
Palpatine: ...I don't know how much longer I can...
Mace: If they do break away...
Palpatine: My negotiations will not fail.
Mace: If they do, you must realize that there aren't enough Jedi to protect the Republic. We're keepers of the peace not soldiers.
Palpatine: Master Yoda, do you really think it will come to war?
Yoda: The dark side clouds everything. Impossible to see, the future is.
Rodian: The loyalist committee has arrived, Chancellor. They await your convenience.
Palpatine: Send them in.
Yoda: Senator Amidala. In grave danger, you are.
Palpatine: Master Jedi, may I suggest the senator be placed under the protection of your graces.
Padme: If I may comment, I don't believe the situation...
Palpatine:...is that serious? Oh but I do [your majesty].
(Rest of scene as you laid out)

Deleting the elevator scene is excellent. That of course brings us to the character of Jar-Jar. I don't think any of us have a clear idea of what we want to do with his character at this point. I do like him commenting on Obi-Wan's beard, though. The rest of the scene is great, and yes Obi-Wan SHOULD call her "Padme." A better transition between this scene and the next with Obi-Wan and Anakin might be some shots of the city (that's what MagnoliaFan did in TCW), but if the fade-to-blacks work well I say keep them as they are nice editing continuity from ANH.

We've already discussed the Ceti Alpha V Eel. It's a good concept, but if it won't blend in seemlessly I say we're best without it. Everthing regarding the Coruscant chase sounds great. I look forward to your music choices as well. If at all possible I'd really like to include "I've heard this lesson before," "You haven't learned anything Anakin." I see no problem with Zam's reference to "bounty hunter" and think it should remain. Those of Jango's profession are referred to as such in ESB.

You seem to have a very clear idea of what you're doing with the dreams. Although I would prefer some consistency in the dreams (from II to III), you've said they will be totally different in style, and I have my reservations on overlaying the dream footage with Anakin in bed, but if you say it works...

Missing Kamino Scene Suggestion:
(Entire library scene)
Jocosta Nu: If an item does not appear in our records, it does not exist!
She walks off, Obi-Wan stares at computer.
Wide shot of Obi-Wan sitting at computer, Yoda (V.O.): The data must have been erased.
CUT to end of Younglings scene, continuing conversation.
Obi-Wan: But Master Yoda who could have erased information from the archives? That's impossible, isn't it?
Yoda: Dangerous and disturbing this puzzle is. Only a Jedi could have erased those files. But who and why, harder to answer. Meditate on this, I will. May the Force be with you.
(I don't see why you altered the end dialogue the way you did. The only problem I could see would be "only a Jedi..." but we're inferring it's Dooku so that won't be a problem. Also w/out that "who and why" don't make any sense. So I say leave the dialogue there as-is).

I think the order of Padme's family scene should be: Arrival, Dinner, Kitchen, Room. Maybe even delete the room scene all together. Portman's delivery is especially flat there, and there's no real appeal to the scene. The "you die if you're unable to adapt" message of course, but still I think it might be best if it was jettisoned. Also putting it before the dinner scene makes little sense as that's when they first talk to the family (at dinner). Surely they would have done so previously on the way to her room. I hope I'm making sense.

I still think replacing "Sypho-Dias" with "Qui-Gon" would be a neat way to do things if appropriate readings by McGregor could be found. Then at the end of the film it could be inferred that Dooku ordered the clones in his former apprentice's name. Too complicated? Maybe. But much more intriguing than the current strategy.

Yes, cut the hair-combing scene in III and utilize the dialogue for the balcony/fireplace scene.

Nute Gunray: we need to establish what exactly we're doing with this character. Is he going to die in I? I'm still not convinced of the logistics of that. That will obviously have a major impact on where we go in II with either him or his brother Carl.

Voice of Qui-Gon: The repeated clip of "Anakin!" is very obvious. Either plug in a different, more subdued reading in the place on the fist one, or just cut it down to one "Anakin!" As for the "No!", in Narnia the Beaver yells "No!" and although it's not Neeson I couldn't help but think how much it sounded like him. That's the best source for an alternate "No!" here I've heard. It would be a shame to have to wait until an official DVD to utilixe it or any of the other great dialogue Neeson has as Aslan...

We've discussed the Battle of Geonosis to death, so I think we've got all that down pretty well.

The ending scene between Dooku and Sidious must be extended one way or another. Establishing who ordered the clones and erased the files if we can. Then there is of course the possible Greivous construction scene. Still in need of greater discussion.

Everything else we've either talked about so much I'm in total agreement or I just dont care anymore.